annotate tools/nlstradamus/nlstradamus.xml @ 3:b2e648e55ed7 draft

Uploaded v0.0.8, MIT licence, RST for README, citation information, development moved to GitHub

<tool id="nlstradamus" name="NLStradamus" version="0.0.8">
    <description>Find nuclear localization signals (NLSs) in protein sequences</description>
    <command>
      NLStradamus -i $fasta_file -t $threshold -m $model -a $algorithm -tab > $tabular_file
    </command>
    <stdio>
        <!-- Assume anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <inputs>
        <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 
        <param name="model" type="select" display="radio" label="Model">
            <option value="1" selected="True">Two state</option>
            <option value="2">Four state</option>
        </param>
        <param name="algorithm" type="select" display="radio" label="Algorithm">
            <option value="0">Viterbi</option>
            <option value="1" selected="True">Posterior with threshold</option>
            <option value="2">Both</option>
        </param>
        <param name="threshold" type="float" label="Posterior theshold" value="0.6">
            <validator type="in_range" min="0" max="1" message="Threshold value should be between 0 and 1."/>
        </param>
    </inputs>
    <outputs>
        <data name="tabular_file" format="tabular" label="NLStradamus results" />
    </outputs>
    <requirements>
        <requirement type="binary">NLStradamus</requirement>
        <requirement type="package" version="1.8">NLStradamus</requirement>
    </requirements>
    <tests>
        <test>
            <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
            <param name="model" value="1" />
            <param name="algorithm" value="1" />
	    <param name="threshold" value="0.6" />
            <output name="tabular_file" file="four_human_proteins.nlstradamus.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="fasta_file" value="empty.fasta" ftype="fasta" />
            <param name="model" value="2" />
            <param name="algorithm" value="2" />
            <param name="threshold" value="0.125"/>
            <output name="tabular_file" file="empty_nlstradamus.tabular" ftype="tabular" />
        </test>
    </tests>
    <help>
    
**What it does**

This calls the NLStradamus tool for prediction of nuclear localization
signals (NLSs), which uses a Hidden Markov Model (HMM).

The input is a FASTA file of protein sequences, and the output is tabular
with six columns (one row per NLS):

====== ===================================================================
Column Description
------ -------------------------------------------------------------------
    c1 Sequence identifier
    c2 Algorithm (posterior or Viterbi)
    c3 Score (probability between threshold and 1 for posterior algorithm)
    c4 Start
    c5 End
    c6 Sequence of NLS
====== ===================================================================

-----

**References**


If you use this Galaxy tool in work leading to a scientific publication please
cite the following papers:

Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
Galaxy tools and workflows for sequence analysis with applications
in molecular plant pathology. PeerJ 1:e167
http://dx.doi.org/10.7717/peerj.167

A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses (2009).
NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction.
BMC Bioinformatics 10(1):202.
http://dx.doi.org/10.1186/1471-2105-10-202

See also http://www.moseslab.csb.utoronto.ca/NLStradamus

This wrapper is available to install into other Galaxy Instances via the Galaxy
Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
    </help>
</tool>